Contacts of the helix formed by residues 165 - 184 (chain D) in PDB entry 4WYV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 165 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ASP* 3.0 12.8 + - - -
164D TYR* 1.3 79.5 - - - +
166D ARG* 1.3 67.2 + - - +
167D PRO 3.3 0.4 - - - -
168D LEU* 3.0 31.9 + - - +
169D HIS* 3.5 21.3 + - - -
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Residues in contact with ARG 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D VAL* 6.0 2.6 - - - +
54D ILE* 5.0 14.1 - - - +
107D TYR* 4.2 21.8 - - - -
108D LEU* 4.4 26.4 + - - +
111D GLU* 4.5 14.9 + - - +
154D LEU* 4.4 14.5 - - - +
158D SER* 3.3 26.7 - - - +
163D ASP* 3.0 21.7 + - - +
165D SER* 1.3 77.8 + - - +
167D PRO* 1.3 64.0 - - + +
169D HIS* 2.9 27.5 + - + +
170D ILE* 2.9 32.4 + - + +
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Residues in contact with PRO 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D SER* 3.5 31.4 - - - +
158D SER* 3.6 9.9 - - - +
159D VAL* 3.9 17.3 - - + -
163D ASP 3.6 7.0 - - - +
164D TYR 3.9 3.1 - - - -
165D SER 3.5 3.1 - - - -
166D ARG* 1.3 94.1 - - + +
168D LEU* 1.3 60.2 - - - +
170D ILE* 3.9 5.1 - - + +
171D SER* 3.0 23.6 + - - -
205D VAL* 4.1 3.1 - - - +
208D VAL* 3.7 20.2 - - + -
209D VAL* 3.6 7.9 - - + +
212D LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D TYR 3.4 19.7 - - - +
165D SER* 3.0 25.9 + - - +
166D ARG 3.0 0.2 + - - -
167D PRO* 1.3 78.5 - - + +
169D HIS* 1.3 70.2 + - + +
171D SER* 3.3 4.7 + - - -
172D THR* 3.2 26.7 + - - +
209D VAL* 4.1 28.0 - - + +
212D LEU* 5.3 5.8 - - + -
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Residues in contact with HIS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D TYR* 3.8 11.8 + - - +
111D GLU* 3.7 33.5 + - - +
165D SER* 3.5 30.9 + - - -
166D ARG* 2.9 16.0 + - + +
168D LEU* 1.3 79.9 - - + +
170D ILE* 1.3 65.2 + - - +
172D THR* 3.2 9.5 + - - -
173D PHE* 3.0 23.6 + - - +
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Residues in contact with ILE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D TYR* 3.6 22.4 - - + +
151D LEU* 3.7 48.0 - - + +
154D LEU* 4.0 16.6 - - + -
155D SER* 4.0 19.7 - - - +
166D ARG* 2.9 37.6 + - + +
167D PRO* 4.1 5.2 - - + +
169D HIS* 1.3 74.3 - - - +
171D SER* 1.3 57.6 + - - +
173D PHE* 3.3 2.9 + - - +
174D ILE* 2.9 38.5 + - + +
205D VAL* 4.1 8.7 - - + -
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PRO 3.0 19.0 + - - -
168D LEU* 3.5 6.1 - - - -
169D HIS 3.2 0.4 - - - -
170D ILE* 1.3 77.2 - - - +
172D THR* 1.3 63.0 + - - +
174D ILE* 3.6 2.1 + - - +
175D ASN* 2.9 39.8 + - - +
205D VAL* 3.3 21.4 - - - +
206D GLU* 3.9 14.4 - - - +
209D VAL* 3.8 16.0 - - - +
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Residues in contact with THR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D LEU 3.2 11.3 + - - +
169D HIS* 3.2 14.2 + - - -
171D SER* 1.3 77.0 - - - +
173D PHE* 1.3 65.8 + - - +
175D ASN* 3.3 6.7 + - - +
176D GLU* 3.0 37.3 + - - +
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Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D TYR* 3.6 28.9 - + + +
111D GLU 4.3 6.1 - - - -
112D THR* 3.8 6.5 - - - -
113D LEU* 3.6 43.5 - - + -
147D LEU* 4.0 15.9 - - + -
151D LEU* 3.5 33.4 - - + -
169D HIS 3.0 16.7 + - - +
170D ILE 3.5 5.6 - - - +
171D SER 3.3 0.2 - - - -
172D THR* 1.3 78.9 + - - +
174D ILE* 1.3 63.9 + - + +
176D GLU* 3.2 19.2 + - + +
177D LEU* 3.1 41.6 + - + +
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Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ALA* 3.6 34.8 - - + +
151D LEU* 4.5 3.1 - - + -
152D SER 4.4 0.4 - - - +
170D ILE* 2.9 31.3 + - + +
171D SER* 4.0 4.7 - - - +
173D PHE* 1.3 81.3 - - + +
175D ASN* 1.3 56.7 + - - +
177D LEU* 3.1 10.9 + - + +
178D ASP* 2.8 27.9 + - - +
198D LEU* 4.4 9.5 - - + +
201D ASP* 4.4 6.7 - - + +
202D VAL* 3.4 35.0 - - + +
205D VAL* 4.1 23.3 - - + -
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Residues in contact with ASN 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D SER* 2.9 33.1 + - - +
172D THR* 3.8 7.3 - - - +
173D PHE 3.3 0.2 - - - -
174D ILE* 1.3 76.2 - - - +
176D GLU* 1.3 57.8 + - - +
178D ASP* 3.8 8.9 + - - +
179D SER* 3.2 29.6 + - - -
202D VAL* 3.7 20.8 - - - +
206D GLU* 3.3 28.4 + - - +
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D THR* 3.0 27.3 + - - +
173D PHE* 3.4 19.5 - - - +
174D ILE 3.2 0.2 - - - -
175D ASN* 1.3 77.2 - - - +
177D LEU* 1.4 58.5 + - + +
179D SER* 3.4 7.0 + - - -
180D GLY* 2.9 24.8 + - - -
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 3.8 28.9 - - + -
144D VAL* 3.9 26.9 - - + +
147D LEU* 5.2 1.1 - - + -
148D ALA* 4.3 25.1 - - + +
173D PHE* 3.1 44.7 + - + +
174D ILE* 3.1 12.4 + - + +
176D GLU* 1.4 73.0 - - + +
178D ASP* 1.3 66.5 + - - +
180D GLY* 3.0 3.5 + - - +
181D PHE* 3.0 39.8 + - + -
198D LEU* 4.4 6.1 - - + -
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ILE 2.8 15.0 + - - +
175D ASN* 3.8 11.9 + - - +
176D GLU 3.3 0.2 - - - -
177D LEU* 1.3 76.4 - - - +
179D SER* 1.3 62.7 + - - +
180D GLY 3.2 0.2 + - - -
181D PHE* 3.2 3.8 + - - +
182D ARG* 3.0 39.3 + - - +
195D TYR* 3.4 18.2 + - - -
198D LEU* 3.8 16.5 - - + +
199D LYS* 5.8 3.2 + - - -
202D VAL* 3.9 28.6 - - + +
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Residues in contact with SER 179 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D ASN 3.2 13.6 + - - -
176D GLU* 3.6 9.9 - - - -
177D LEU 3.3 0.2 - - - -
178D ASP* 1.3 78.6 - - - +
180D GLY* 1.3 63.2 + - - +
182D ARG* 3.1 25.5 - - - +
183D LEU* 3.4 14.6 + - - +
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D GLU 2.9 14.4 + - - -
177D LEU* 3.0 7.0 + - - -
179D SER* 1.3 77.7 - - - +
181D PHE* 1.3 61.5 + - - +
183D LEU* 3.2 27.0 + - - +
184D LEU* 3.7 9.9 + - - +
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Residues in contact with PHE 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 4.1 37.5 - - + -
144D VAL* 4.5 16.2 - - + -
145D LEU* 3.5 43.1 - - + -
177D LEU* 3.0 32.2 + - + -
178D ASP 3.2 2.2 + - - +
180D GLY* 1.3 72.2 - - - +
182D ARG* 1.3 59.4 + - - +
184D LEU* 2.8 47.3 + - + +
186D LEU* 4.3 15.8 - - + +
191D LEU* 5.4 0.9 - - + -
195D TYR* 3.2 36.6 - + + -
198D LEU* 3.9 12.8 - - + -
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Residues in contact with ARG 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ASP* 3.0 36.2 + - - +
179D SER* 3.1 18.4 - - - +
181D PHE* 1.3 76.8 - - - +
183D LEU* 1.3 65.6 + - + +
184D LEU 3.3 6.9 + - - +
195D TYR* 3.7 23.2 + - - +
199D LYS* 6.2 2.0 - - - +
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D SER* 3.4 14.4 + - - +
180D GLY* 3.2 15.5 + - - +
181D PHE 3.2 0.2 - - - -
182D ARG* 1.3 81.9 - - + +
184D LEU* 1.3 65.1 + - + +
185D ASN* 3.6 4.0 + - - +
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.7 36.6 - - + -
180D GLY 3.8 12.6 - - - +
181D PHE* 2.8 38.8 + - + +
182D ARG 3.3 7.7 - - - +
183D LEU* 1.3 79.3 - - + +
185D ASN* 1.3 60.1 + - - +
186D LEU* 3.4 20.8 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il